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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ), 'gf_id' => 'HOM05D001393', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001393' ), 'data_identifier' => 'HOM05D001393', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001393', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33980' => 'bna', 'A05p05660' => 'bna', 'A06p39440' => 'bna', 'A07p25310' => 'bna', 'A09p04300' => 'bna', 'A09p53160' => 'bna', 'Aa31LG10G15190' => 'aar', 'Aa31LG11G7400' => 'aar', 'Aa31LG3G14230' => 'aar', 'Aa31LG3G14240' => 'aar', 'Aa31LG3G14660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1995' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1998' => 'aag', 'Actinidia21547' => 'ach', 'Ah.10g038790' => 'amhyb', 'Ah.10g038800' => 'amhyb', 'AL4G44890' => 'aly', 'AL5G43330' => 'aly', 'AL5G43340' => 'aly', 'AL8G20040' => 'aly', 'Aqoxy1G00280' => 'aox', 'Aqoxy3G01287' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1C19KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BH8J5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4Q3NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G3L9EH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N199JY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RM2YS3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6CP9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VWB10K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUV7WX' => 'arhy', 'AT2G45710' => 'ath', 'AT3G61110' => 'ath', 'AT3G61111' => 'ath', 'AT5G47930' => 'ath', 'AT5G47940' => 'ath', 'ATR0332G069' => 'atr', 'ATR0824G178' => 'atr', 'Atru.chr11.2612' => 'acertr', 'Atru.chr6.2714' => 'acertr', 'AUR62007034' => 'cqu', 'AUR62009391' => 'cqu', 'AUR62019898' => 'cqu', 'AUR62023073' => 'cqu', 'AUR62037800' => 'cqu', 'BcaB02g07389' => 'bca', 'BcaB06g29429' => 'bca', 'BcaB07g29999' => 'bca', 'BcaC01g05110' => 'bca', 'BcaC03g17622' => 'bca', 'BcaC04g23798' => 'bca', 'BcaC06g30834' => 'bca', 'BcaC07g40613' => 'bca', 'BcaC07g42653' => 'bca', 'BcaC08g45099' => 'bca', 'BcaC08g45102' => 'bca', 'BolC2t11678H' => 'bol', 'BolC3t15372H' => 'bol', 'BolC4t22284H' => 'bol', 'BolC6t37879H' => 'bol', 'BolC6t37883H' => 'bol', 'BolC6t37884H' => 'bol', 'BolC7t44402H' => 'bol', 'BolC8t51176H' => 'bol', 'BolC9t53385H' => 'bol', 'BraA02t08706Z' => 'bra', 'BraA03t11738Z' => 'bra', 'BraA04t18859Z' => 'bra', 'BraA06t26859Z' => 'bra', 'BraA07t30174Z' => 'bra', 'BraA09t36067Z' => 'bra', 'BraA09t40742Z' => 'bra', 'C02p56230' => 'bna', 'C02p58440' => 'bna', 'C04p06620' => 'bna', 'C04p71780' => 'bna', 'C06p27070' => 'bna', 'C06p27110' => 'bna', 'C07p38830' => 'bna', 'C08p35880' => 'bna', 'C08p35930' => 'bna', 'C09p04570' => 'bna', 'CAN.G1513.5' => 'can', 'CAN.G624.5' => 'can', 'CANSAT56G0661' => 'cansat', 'CANSAT56G1190' => 'cansat', 'CANSAT56G1835' => 'cansat', 'CANSAT56G2834' => 'cansat', 'CANSAT80G1121' => 'cansat', 'CARHR140950' => 'chi', 'CARHR171400' => 'chi', 'CARHR184320' => 'chi', 'CARHR184330' => 'chi', 'Carub.0004s2837' => 'cru', 'Carub.0005s2775' => 'cru', 'Carub.0008s0749' => 'cru', 'Carub.0011s0010' => 'cru', 'Carub.0011s0011' => 'cru', 'Ca_00423_v3' => 'car', 'Ca_19581_v3' => 'car', 'Ca_20942_v3' => 'car', 'Ca_25661_v3' => 'car', 'Ca_30298_v3' => 'car', 'CBR_g40843' => 'cbr', 'Cc00_g04030' => 'ccan', 'Cc02_g28120' => 'ccan', 'Cc11_g14900' => 'ccan', 'CDE02G0642' => 'cde', 'CDE05G0268' => 'cde', 'CDE05G2003' => 'cde', 'CDE05G2132' => 'cde', 'CDE06G0493' => 'cde', 'Cfa007155' => 'cfa', 'Cfa010777' => 'cfa', 'Ciclev10017332m.g' => 'ccl', 'Ciclev10017335m.g' => 'ccl', 'Ciclev10017430m.g' => 'ccl', 'Ciclev10017799m.g' => 'ccl', 'Ciclev10030722m.g' => 'ccl', 'CiPaw.05G099900' => 'cil', 'CiPaw.14G000700' => 'cil', 'ClCG01G007900' => 'cla', 'ClCG06G001690' => 'cla', 'ClCG09G004070' => 'cla', 'COL.COLO4_04862' => 'col', 'COL.COLO4_10472' => 'col', 'COL.COLO4_13393' => 'col', 'COL.COLO4_21844' => 'col', 'Cpa.g.sc125.11' => 'cpa', 'Cpa.g.sc70.49' => 'cpa', 'Cpa.g.sc70.87' => 'cpa', 'Cre02.g145250' => 'cre', 'Cre12.g529400' => 'cre', 'CsaV3_5G025010' => 'csa', 'CsaV3_6G007700' => 'csa', 'CsaV3_7G030970' => 'csa', 'CSS0004092' => 'camsi', 'CSS0035450' => 'camsi', 'CSS0038724' => 'camsi', 'DCAR_003251' => 'dca', 'DCAR_005493' => 'dca', 'DCAR_014461' => 'dca', 'DCAR_022338' => 'dca', 'DCAR_029678' => 'dca', 'Dinv03900' => 'din', 'Dinv09348' => 'din', 'Dinv26264' => 'din', 'Dinv33268' => 'din', 'Dinv43433' => 'din', 'Dinv43434' => 'din', 'Dinv43435' => 'din', 'Duzib106G1543' => 'dzi', 'Duzib128G2012' => 'dzi', 'Duzib133G0545' => 'dzi', 'Duzib138G0028' => 'dzi', 'Duzib138G1268' => 'dzi', 'Duzib138G1437' => 'dzi', 'Duzib177G0585' => 'dzi', 'Duzib187G0372' => 'dzi', 'ECA233G0832' => 'eca', 'ECA234G3133' => 'eca', 'ECA248G1228' => 'eca', 'EL10Ac2g04339' => 'bvu', 'EL10Ac6g13890' => 'bvu', 'EL10As2g23278' => 'bvu', 'Eucgr.E03676' => 'egr', 'Eucgr.J01280' => 'egr', 'Eucgr.J01288' => 'egr', 'FAN01G2686' => 'fan', 'FAN03G1765' => 'fan', 'FAN03G3510' => 'fan', 'FAN06G3336' => 'fan', 'FAN07G1509' => 'fan', 'FAN07G1857' => 'fan', 'FAN10G3273' => 'fan', 'FAN12G0601' => 'fan', 'FAN12G2525' => 'fan', 'FAN19G1529' => 'fan', 'FAN23G1213' => 'fan', 'FvH4_1g27030' => 'fve', 'FvH4_4g22340' => 'fve', 'FvH4_4g22990' => 'fve', 'FvH4_5g06191' => 'fve', 'FvH4_7g01170' => 'fve', 'Glyma.02G067300' => 'gma', 'Glyma.02G067400' => 'gma', 'Glyma.09G228900' => 'gma', 'Glyma.12G007700' => 'gma', 'Glyma.16G046500' => 'gma', 'Glyma.16G148500' => 'gma', 'Glyma.19G105700' => 'gma', 'Gohir.A07G083800' => 'ghi', 'Gohir.A07G165000' => 'ghi', 'Gohir.A08G050500' => 'ghi', 'Gohir.A08G143900' => 'ghi', 'Gohir.A08G209900' => 'ghi', 'Gohir.A11G265700' => 'ghi', 'Gohir.A13G173900' => 'ghi', 'Gohir.D03G054450' => 'ghi', 'Gohir.D07G089900' => 'ghi', 'Gohir.D07G177100' => 'ghi', 'Gohir.D08G060300' => 'ghi', 'Gohir.D08G164900' => 'ghi', 'Gohir.D08G226800' => 'ghi', 'Gohir.D10G094250' => 'ghi', 'Gohir.D11G275800' => 'ghi', 'Gohir.D13G179600' => 'ghi', 'Gorai.001G096100' => 'gra', 'Gorai.001G197900' => 'gra', 'Gorai.003G057100' => 'gra', 'Gorai.004G062400' => 'gra', 'Gorai.004G171900' => 'gra', 'Gorai.004G240700' => 'gra', 'Gorai.007G298000' => 'gra', 'Gorai.011G103600' => 'gra', 'Gorai.013G205000' => 'gra', 'GSVIVG01001113001' => 'vvi', 'GSVIVG01032121001' => 'vvi', 'GSVIVG01032964001' => 'vvi', 'HanXRQChr06g0175431' => 'han', 'HanXRQChr08g0210461' => 'han', 'HanXRQChr09g0251311' => 'han', 'HanXRQChr12g0362521' => 'han', 'HanXRQChr17g0540551' => 'han', 'Haze_12516' => 'cav', 'Haze_14965' => 'cav', 'Haze_19867' => 'cav', 'Haze_27114' => 'cav', 'Hma1.2p1_0152F.1_g067780' => 'hma', 'Hma1.2p1_0738F.1_g210830' => 'hma', 'HPP92_015712' => 'vpl', 'HPP92_020114' => 'vpl', 'HPP92_021610' => 'vpl', 'HPP92_026649' => 'vpl', 'Hund15256' => 'sun', 'Hund21482' => 'sun', 'Hund22193' => 'sun', 'Lalb_Chr02g0156881' => 'lal', 'Lalb_Chr04g0252381' => 'lal', 'Lalb_Chr10g0103231' => 'lal', 'Lalb_Chr14g0363611' => 'lal', 'Lalb_Chr17g0344961' => 'lal', 'Lalb_Chr19g0140311' => 'lal', 'Lalb_Chr21g0316941' => 'lal', 'Lj1g0027586' => 'lja', 'Lj3g0000057' => 'lja', 'Lj5g0001186' => 'lja', 'Lj9A633T62' => 'lonja', 'Lsat_1_v5_gn_1_106561' => 'lsa', 'Lsat_1_v5_gn_1_44501' => 'lsa', 'Lsat_1_v5_gn_3_33000' => 'lsa', 'Lsat_1_v5_gn_4_96541' => 'lsa', 'Lsat_1_v5_gn_5_190500' => 'lsa', 'Lsat_1_v5_gn_5_6460' => 'lsa', 'Lsat_1_v5_gn_7_94561' => 'lsa', 'Lsat_1_v5_gn_8_83181' => 'lsa', 'Manes.06G017200' => 'mes', 'Manes.08G100000' => 'mes', 'Manes.09G173400' => 'mes', 'Manes.10G141000' => 'mes', 'Mapoly0095s0009' => 'mpo', 'MBI04_g36081_MAGBIO' => 'mbi', 'MBI07_g07564_MAGBIO' => 'mbi', 'MBI07_g13956_MAGBIO' => 'mbi', 'MBI11_g02481_MAGBIO' => 'mbi', 'MCO16G246' => 'mco', 'MD00G1067000' => 'mdo', 'MD00G1112200' => 'mdo', 'MD02G1283100' => 'mdo', 'MD02G1309200' => 'mdo', 'MD05G1179000' => 'mdo', 'MD07G1012500' => 'mdo', 'MD08G1164100' => 'mdo', 'MD13G1127700' => 'mdo', 'MD13G1132700' => 'mdo', 'MD15G1319300' => 'mdo', 'MD16G1127800' => 'mdo', 'MD16G1143000' => 'mdo', 'Medtr1g111970' => 'mtr', 'Medtr2g015680' => 'mtr', 'Medtr2g029270' => 'mtr', 'Medtr4g037495' => 'mtr', 'MELO3C005089.2' => 'cme', 'MELO3C022363.2' => 'cme', 'MELO3C023559.2' => 'cme', 'MELO3C032659.2' => 'cme', 'MELO3C035161.2' => 'cme', 'Migut.D00169' => 'egut', 'Migut.G01189' => 'egut', 'Migut.G01197' => 'egut', 'Migut.N00832' => 'egut', 'Migut.N01605' => 'egut', 'MSTRG.22025' => 'ama', 'MSTRG.28063' => 'ama', 'MSTRG.441' => 'ama', 'MSTRG.5028' => 'ama', 'Nitab4.5_0000001g0230' => 'nta', 'Nitab4.5_0000069g0500' => 'nta', 'Nitab4.5_0001123g0030' => 'nta', 'Nitab4.5_0001761g0330' => 'nta', 'Nitab4.5_0002199g0050' => 'nta', 'Nitab4.5_0002569g0080' => 'nta', 'Nitab4.5_0005286g0040' => 'nta', 'Nitab4.5_0007345g0040' => 'nta', 'Nitab4.5_0011787g0010' => 'nta', 'Nn2g15307' => 'nnu', 'Nn3g16242' => 'nnu', 'Nn7g36401' => 'nnu', 'Oeu026775.1' => 'oeu', 'Oeu035279.1' => 'oeu', 'Oeu048683.1' => 'oeu', 'Oeu049495.1' => 'oeu', 'Oeu062520.1' => 'oeu', 'Os02g0478700' => 'osa', 'Os04g0346100' => 'osa', 'Os04g0399000' => 'osa', 'Os07g0569000' => 'osa', 'Peaxi162Scf00097g01217' => 'pax', 'Peaxi162Scf00152g01336' => 'pax', 'Peaxi162Scf00207g00234' => 'pax', 'Peaxi162Scf00842g00420' => 'pax', 'PGR044G2234' => 'pgr', 'PGR102G2928' => 'pgr', 'PGR119G0258' => 'pgr', 'PGR142G2083' => 'pgr', 'PGSC0003DMG400016367' => 'stu', 'PGSC0003DMG401023992' => 'stu', 'PGSC0003DMG401028933' => 'stu', 'Phvul.001G079100' => 'pvu', 'Phvul.004G069100' => 'pvu', 'Phvul.011G009600' => 'pvu', 'Potri.001G069100' => 'ptr', 'Potri.001G265100' => 'ptr', 'Potri.003G161200' => 'ptr', 'Potri.006G192900' => 'ptr', 'Potri.009G060000' => 'ptr', 'Pp3c11_17310' => 'ppa', 'Pp3c18_2100' => 'ppa', 'Pp3c1_15840' => 'ppa', 'Pp3c21_21540' => 'ppa', 'Pp3c22_18310' => 'ppa', 'Pp3c2_20540' => 'ppa', 'Pp3c5_15230' => 'ppa', 'PRCOL_00002588' => 'pco', 'Prupe.1G212900' => 'ppe', 'Prupe.1G218300' => 'ppe', 'Prupe.2G015000' => 'ppe', 'Psat0s4121g0120' => 'psa', 'Psat1g169400' => 'psa', 'Psat1g199080' => 'psa', 'Psat6g057640' => 'psa', 'Psat7g196360' => 'psa', 'PSO017G0088' => 'pso', 'PSO151G0037' => 'pso', 'PSO339G2815' => 'pso', 'PSO339G5226' => 'pso', 'PSO384G0142' => 'pso', 'PSO478G3775' => 'pso', 'PSO541G3297' => 'pso', 'PSO675G3311' => 'pso', 'QL02p068815' => 'qlo', 'QL02p086813' => 'qlo', 'QL04p008271' => 'qlo', 'RcHm_v2.0_Chr1g0316471' => 'rch', 'RcHm_v2.0_Chr3g0487351' => 'rch', 'RcHm_v2.0_Chr4g0428571' => 'rch', 'RcHm_v2.0_Chr4g0429251' => 'rch', 'Rhsim12G0100800' => 'rsi', 'Sabra01G0048400' => 'sbr', 'Sabra03G0117200' => 'sbr', 'Sabra06G0148200' => 'sbr', 'Sabra09G0044200' => 'sbr', 'Sabra16G0162900' => 'sbr', 'SalBow2G1468' => 'sbo', 'SalBow3G1380' => 'sbo', 'SalBow3G2800' => 'sbo', 'SalBow3G4439' => 'sbo', 'SalBow3G4536' => 'sbo', 'SalBow4G1412' => 'sbo', 'SalBow6G6124' => 'sbo', 'SalBow7G3555' => 'sbo', 'SalBow7G3650' => 'sbo', 'SalBow7G4183' => 'sbo', 'Sc07g0003890' => 'sci', 'Sc11g0009120' => 'sci', 'Sed0005297' => 'sed', 'Sed0007124' => 'sed', 'Sed0015725' => 'sed', 'Sed0017511' => 'sed', 'Sed0020202' => 'sed', 'SGA_v2.0_scaffold161G37810' => 'sas', 'SGA_v2.0_scaffold161G37811' => 'sas', 'SGA_v2.0_scaffold5G02964' => 'sas', 'SMO196G0276' => 'smo', 'SMO367G0051' => 'smo', 'Solyc01g008080.3' => 'sly', 'Solyc01g008090.4' => 'sly', 'Solyc06g068710.3' => 'sly', 'Solyc11g007060.2' => 'sly', 'Solyc11g020150.1' => 'sly', 'Solyc11g020350.1' => 'sly', 'Solyc11g020490.3' => 'sly', 'Sopen01g003640' => 'spe', 'Sopen06g025990' => 'spe', 'Sopen11g002980' => 'spe', 'Sp2g18430' => 'spa', 'Sp2g18440' => 'spa', 'Sp4g27760' => 'spa', 'Sp5g02270' => 'spa', 'TAR374G0046' => 'tar', 'TAR622G0771' => 'tar', 'TAR623G0231' => 'tar', 'TAR623G1737' => 'tar', 'THA.LOC104799991' => 'tha', 'THA.LOC104801434' => 'tha', 'THA.LOC104802009' => 'tha', 'THA.LOC104807231' => 'tha', 'THA.LOC104816698' => 'tha', 'Thecc.01G179000' => 'tca', 'Thecc.01G409700' => 'tca', 'Thecc.04G049700' => 'tca', 'Thecc.05G309900' => 'tca', 'Thhalv10001700m.g' => 'esa', 'Thhalv10003674m.g' => 'esa', 'Thhalv10005209m.g' => 'esa', 'Thhalv10006345m.g' => 'esa', 'Thhalv10009228m.g' => 'esa', 'TPR.G11654' => 'tpr', 'TPR.G3660' => 'tpr', 'TWI09G0484' => 'twi', 'TWI18G0127' => 'twi', 'TWI36G0837' => 'twi', 'TWI38G0079' => 'twi', 'TWI38G0116' => 'twi', 'TWI63G0076' => 'twi', 'TWI73G0713' => 'twi', 'TWI75G1768' => 'twi', 'unitig_26.g10434' => 'ugi', 'unitig_578.g16692' => 'ugi', 'unitig_747.g21108' => 'ugi', 'unitig_749.g13334' => 'ugi', 'vmacro13675' => 'vma', 'vmacro16069' => 'vma', 'vmacro18396' => 'vma', 'VMungo1127G2137' => 'vmu', 'Zm00001eb107220' => 'zma', 'Zm00001eb202910' => 'zma', 'Zm00001eb214990' => 'zma', 'Zm00001eb241090' => 'zma', 'Zm00001eb324710' => 'zma' ) $gf_id = 'HOM05D001393' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001393' ) $data_identifier = 'HOM05D001393' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 1, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 2, 'sed' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 2, 'twi' => (int) 8, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 1, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb324710' $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